Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
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Major publications by the team in recent years
M. Avalos, H. Pouyes, Y. Grandvalet, L. ORRIOLS, E. Lagarde.
Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm, in: BMC Bioinformatics, 2015, vol. 16, no Suppl 6, S1 p. [ DOI : 10.1186/1471-2105-16-S6-S1 ]
D. Commenges, A. Gégout-Petit.
The stochastic system approach for estimating dynamic treatments effect, in: Lifetime Data Analysis, 2015, 18 p. [ DOI : 10.1007/s10985-015-9322-3 ]
D. Commenges, H. Jacqmin-Gadda.
Dynamical Biostatistical Models, Chapman and Hall/CRC, October 2015.
B. P. Hejblum, J. Skinner, R. Thiébaut.
Time-Course Gene Set Analysis for Longitudinal Gene Expression Data, in: PLoS Computational Biology, 2015, vol. 11, no 6, e1004310 p. [ DOI : 10.1371/journal.pcbi.1004310 ]
C. C. Iwuji, J. Orne-Gliemann, J. Larmarange, N. Okesola, F. Tanser, R. Thiebaut, C. Rekacewicz, M.-L. Newell, F. Dabis, N. Low.
Uptake of Home-Based HIV Testing, Linkage to Care, and Community Attitudes about ART in Rural KwaZulu-Natal, South Africa: Descriptive Results from the First Phase of the ANRS 12249 TasP Cluster-Randomised Trial, in: PLoS Medicine, August 2016, vol. 13, no 8.
R. Le Grand, N. Dereuddre-Bosquet, S. Dispinseri, L. Gosse, D. Desjardins, X. Shen, M. Tolazzi, C. Ochsenbauer, H. Saidi, G. Tomaras, M. Prague, S. W. Barnett, R. Thiebaut, A. Cope, G. Scarlatti, R. J. Shattock, G. Silvestri.
Superior Efficacy of a Human Immunodeficiency Virus Vaccine Combined with Antiretroviral Prevention in Simian-Human Immunodeficiency Virus-Challenged Nonhuman Primates, in: Journal of Virology, May 2016, vol. 90, no 11, pp. 5315 - 5328.
E. Lhomme, L. Richert, Z. Moodie, C. Pasin, S. A. Kalams, C. Morgan, S. Self, S. C. De Rosa, R. Thiébaut.
Early CD4+ T Cell Responses Are Associated with Subsequent CD8+ T Cell Responses to an rAd5-Based Prophylactic Prime-Boost HIV Vaccine Strategy, in: PLoS ONE, April 2016, vol. 11, no 4.
B. Liquet, P. Lafaye De Micheaux, B. P. Hejblum, R. Thiébaut.
Group and sparse group partial least square approaches applied in genomics context, in: Bioinformatics, 2016, vol. 32, no 1, pp. 35-42. [ DOI : 10.1093/bioinformatics/btv535 ]
S. M. Moyo, T. M. Mohammed, K. M. Wirth, M. M. Prague, K. M. Bennett, M. P. Holme, L. M. Mupfumi, P. M. Sebogodi, N. M. Moraka, C. M. Boleo, C. M. Maphorisa, B. M. Seraise, S. M. Gaseitsiwe, R. M. Musonda, E. M. Van Widenfelt, K. M. Powis, T. M. Gaolathe, E. M. Tchetgen Tchetgen, J. M. Makhema, M. M. Essex, S. M. Lockman, V. M. Novitsky.
Point-of-Care Cepheid Xpert HIV-1 Viral Load Test in Rural African Communities Is Feasible and Reliable, in: Journal of Clinical Microbiology, 2016, vol. 54, no 12, pp. 3050 - 3055. [ DOI : 10.1128/JCM.01594-16 ]
F. Nakagawa, A. Van Sighem, R. Thiebaut, C. Smith, O. Ratmann, V. Cambiano, J. Albert, A. Amato-Gauci, D. Bezemer, C. Campbell, D. Commenges, M. Donoghoe, D. Ford, R. Kouyos, R. Lodwick, J. Lundgren, N. Pantazis, A. Pharris, C. Quinten, C. Thorne, G. Touloumi, V. Delpech, A. Phillips.
A method to estimate the size and characteristics of HIV-positive populations using an individual-based stochastic simulation model, in: Epidemiology, 2016, vol. 27, no 2, pp. 247-256. [ DOI : 10.1097/EDE.0000000000000423 ]
L. Richert, E. Lhomme, C. Fagard, Y. Levy, G. Chêne, R. Thiébaut.
Recent developments in clinical trial designs for HIV vaccine research, in: Human vaccines & immunotherapeutics, 2015, vol. 11, no 4, pp. 1022–9. [ DOI : 10.1080/21645515.2015.1011974 ]
P. Schommers, G. Martrus, U. Matschl, M. Sirignano, M. Lütgehetmann, L. Richert, T. J. Hope, G. Fätkenheuer, M. Altfeld, F. Kirchhoff.
Changes in HIV-1 Capsid Stability Induced by Common Cytotoxic-T-Lymphocyte-Driven Viral Sequence Mutations, in: Journal of Virology, July 2016, vol. 90, no 16, pp. 7579 - 7586. [ DOI : 10.1128/JVI.00867-16 ]
M. Surenaud, C. Manier, L. Richert, R. Thiébaut, Y. Levy, S. Hue, C. Lacabaratz.
Optimization and evaluation of Luminex performance with supernatants of antigen-stimulated peripheral blood mononuclear cells, in: BMC Immunology, December 2015, vol. 17, no 1, 44 p. [ DOI : 10.1186/s12865-016-0182-8 ]
R. Thiébaut, J. Drylewicz, M. Prague, C. Lacabaratz, S. Beq, A. Jarne, T. Croughs, R.-P. Sekaly, M. M. Lederman, I. Sereti, D. Commenges, Y. Lévy.
Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+ T Cells in HIV-1 Infection, in: PLoS computational biology, 2014, vol. 10, no 5, e1003630.
R. Thiébaut, A. Jarne, J.-P. Routy, I. Sereti, M. Fischl, P. Ive, R. F. Speck, G. D'Offizi, S. Casari, D. Commenges, S. Foulkes, V. Natarajan, T. Croughs, J.-F. Delfraissy, G. Tambussi, Y. Levy, M. M. Lederman.
Repeated Cycles of Recombinant Human Interleukin 7 in HIV-Infected Patients With Low CD4 T-Cell Reconstitution on Antiretroviral Therapy: Results of 2 Phase II Multicenter Studies, in: Clinical Infectious Diseases, May 2016, vol. 62, no 9, pp. 1178 - 1185.
Publications of the year

Articles in International Peer-Reviewed Journals

D. Agniel, B. P. Hejblum.
Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, in: Biostatistics, 2017, vol. 18, no 4, pp. 589-604, [ DOI : 10.1093/biostatistics/kxx005 ]
V. Bouteloup, C. Sabin, A. Mocroft, L. Gras, N. Pantazis, V. Le Moing, A. D'Arminio Monforte, M. Mary-Krause, R. Roca, J. M. Miro, M. Battegay, N. H. Brockmeyer, M. Berenguer, P. Morlat, C. Obel, S. De Wit, G. Fätkenheuer, R. Zangerle, J. Ghosn, R. Pérez-Hoyos, M. Campbell, C. Prins, G. Chêne, L. Meyer, M. Dorrucci, C. Torti, R. Thiébaut.
Reference curves for CD4 T-cell count response to combination antiretroviral therapy in HIV-1-infected treatment-naïve patients, in: HIV Medicine, 2017, vol. 18, no 1, pp. 33 - 44. [ DOI : 10.1111/hiv.12389 ]
R. Genuer, J.-M. Poggi, C. Tuleau-Malot, N. Villa-Vialaneix.
Random Forests for Big Data, in: Big Data Research, September 2017, vol. 9, pp. 28-46, [ DOI : 10.1016/j.bdr.2017.07.003 ]
B. P. Hejblum, J. Cui, L. J. Lahey, A. Cagan, J. A. Sparks, J. Sokolove, T. Cai, K. P. Liao.
Association between anti-citrullinated fibrinogen antibodies and coronary artery disease in rheumatoid arthritis, in: Arthritis Care & Research, 2017, forthcoming. [ DOI : 10.1002/acr.23444 ]
P. Hellard, C. Scordia, M. F. Avalos, I. Mujika, P. David.
Modelling of optimal training load patterns during the 11 weeks preceding major competition in elite swimmers, in: Applied Physiology, Nutrition, and Metabolism, 2017.
A. Jarne, D. Commenges, M. Prague, Y. Levy, R. Thiébaut.
Modeling CD4 + T cells dynamics in HIV-infected patients receiving repeated cycles of exogenous Interleukin 7, in: Annals Of Applied Statistics, June 2017.
K. Liao, J. A. Sparks, B. P. Hejblum, I.-H. Kuo, J. Cui, L. J. Lahey, A. Cagan, V. S. Gainer, W. Liu, T. T. Cai, J. Sokolove, T. Cai.
Phenome-Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis, in: Arthritis & rheumatology, April 2017, vol. 69, no 4, pp. 742 - 749. [ DOI : 10.1002/art.39974 ]
F. Mougin, D. Auber, R. Bourqui, G. Diallo, I. Dutour, V. Jouhet, F. Thiessard, R. Thiebaut, P. Thebault.
Visualizing omics and clinical data: which challenges for dealing with their variety?, in: Methods, 2017. [ DOI : 10.1016/j.ymeth.2017.08.012 ]
N. Mélanie, M. F. Avalos, A. LUXCEY, B. Contrand, L. R. Salmi, A. Fourrier-Reglat, B. Gadegbeku, E. Lagarde, L. ORRIOLS.
Prescription medicine use by pedestrians and the risk of injurious road traffic crashes: A case-crossover study, in: PLoS Medicine, 2017.
M.-Q. Picat, I. Pellegrin, J. Bitard, L. Wittkop, C. Proust-Lima, B. Liquet, J.-F. Moreau, F. Bonnet, P. Blanco, R. Thiébaut.
Integrative Analysis of Immunological Data to Explore Chronic Immune T-Cell Activation in Successfully Treated HIV Patients, in: PLoS ONE, January 2017, vol. 12, no 1. [ DOI : 10.1371/journal.pone.0169164 ]
M. Prague, D. Commenges, J. M. Gran, B. Ledergerber, J. Young, H. Furrer, R. Thiébaut.
Dynamic models for estimating the effect of HAART on CD4 in observational studies: Application to the Aquitaine Cohort and the Swiss HIV Cohort Study, in: Biometrics, March 2017, vol. 73, no 1, pp. 294 - 304. [ DOI : 10.1111/biom.12564 ]
M. Prague, E. Turner, l. Fan, G. John, M. David.
Review of recent Methodological Developments in group-randomized trials: Part 1 - Design, in: American Journal of Public Health, June 2017.
M. Prague, E. Turner, G. John, l. Fan, M. David.
Review of recent Methodological Developments in group-randomized trials: Part 2 - Analysis, in: American Journal of Public Health, June 2017.
M. Prague, R. Wang, V. de Gruttola.
CRTgeeDR: An R Package for Doubly Robust Generalized Estimating Equations Estimations in Cluster Randomized Trials with Missing Data, in: R journal, September 2017.
A. Rechtien, L. Richert, H. Lorenzo, G. Martrus, B. P. Hejblum, C. Dahlke, R. Kasonta, M. Zinser, H. Stubbe, U. Matschl, A. Lohse, V. Krähling, M. Eickmann, S. Becker, R. Thiébaut, M. Altfeld, M. Addo.
Systems Vaccinology Identifies an Early Innate Immune Signature as a Correlate of Antibody Responses to the Ebola Vaccine rVSV-ZEBOV, in: Cell Reports , 2017, vol. 20, no 9, pp. 2251 - 2261. [ DOI : 10.1016/j.celrep.2017.08.023 ]
M. Tabue-Teguo, L. Grasset, J. A. Avila-Funes, R. Genuer, C. Proust-Lima, K. Pérès, C. Feart, H. Amieva, M. G.-C. Harmand, C. Helmer, N. Salles, M. Rainfray, J. F. Dartigues.
Prevalence and Co-Occurrence of Geriatric Syndromes in People Aged 75 Years and Older in France: Results From the Bordeaux Three-city Study, in: Journals of Gerontology, Series A, May 2017. [ DOI : 10.1093/gerona/glx068 ]
R. Thiebaut, S. Hue, F. Le Marec, J.-D. Lelievre, M. Dupon, E. Foucat, E. Lazaro, F. Dabis, P. Duffau, L. Wittkop, M. Surenaud, I. Pellegrin, C. Lacabaratz, F. Bonnet, Y. Lévy.
Serum ST2 level is an independent predictor of all-cause mortality in HIV-infected patients. Aquitaine Cohort, France, in: AIDS, 2017.
R. Thiebaut, F. Thiessard.
Public Health and Epidemiology Informatics, in: IMIA Yearbook of Medical Informatics, 2017. [ DOI : 10.15265/IY-2017-035 ]
L. Zago, P.-Y. Hervé, R. Genuer, A. Laurent, B. Mazoyer, N. Tzourio-Mazoyer, M. Joliot.
Predicting hemispheric dominance for language production in healthy individuals using support vector machine, in: Human Brain Mapping, September 2017. [ DOI : 10.1002/hbm.23770 ]

National Conferences with Proceedings

M. Prague, R. Thiébaut, P. Moireau, A. Collin.
Joint-state and parameters estimation using nudging and SEIK filters for HIV mechanistic models, in: Journée de la statistique francaise, Avignon, France, June 2017.

Conferences without Proceedings

H. Lorenzo, R. Thiebaut, J. Saracco.
Multi-block high-dimensional lasso-penalized analysis with imputation of missing data applied to postgenomic data in an Ebola vaccine trial, in: Annual workshop on Statistical Methods for Post Genomic Data - SMPGD 2018, Montpellier, France, January 2018.
P. Soret, M. F. Avalos, S. Cheng, R. Thiebaut.
High-dimensional compositional microbiota data: state-of-the-art of methods and software implementations, in: 2017 - GDR « Statistiques et santé », Bordeaux, France, October 2017.

Other Publications

R. Genuer, J.-M. Poggi.
Arbres CART et Forêts aléatoires,Importance et sélection de variables, January 2017, working paper or preprint.
B. P. Hejblum, C. Alkhassim, R. Gottardo, F. Caron, R. Thiébaut.
Sequential Dirichlet Process Mixtures of Multivariate Skew t-distributions for Model-based Clustering of Flow Cytometry Data, August 2017, - 39 pages, 11 figures.
M. ´. Prague, D. Commenges, R. Thiébaut.
In Silico Evaluation of HIV Short-cycle Therapies with Dynamical Models, August 2017, Keystone Symposium , Poster.
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